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P38203

- LSM2_YEAST

UniProt

P38203 - LSM2_YEAST

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Protein
U6 snRNA-associated Sm-like protein LSm2
Gene
LSM2, SMX5, SNP3, YBL026W, YBL0425
Organism
Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast)
Status
Reviewed - Annotation score: 5 out of 5 - Experimental evidence at protein leveli

Functioni

Component of LSm protein complexes, which are involved in RNA processing and may function in a chaperone-like manner. Component of the cytoplasmic LSM1-LSM7 complex which is involved in mRNA degradation by activating the decapping step. Component of the nuclear LSM2-LSM8 complex, which is involved in splicing of nuclear mRNAs. LSM2-LSM8 associates with multiple snRNP complexes containing the U6 snRNA (U4/U6 snRNP, U4/U6.U5 snRNP, and free U6 snRNP). It binds directly to the U6 snRNA and plays a role in the biogenesis and stability of the U6 snRNP and U4/U6 snRNP complexes. It probably also is involved degradation of nuclear pre-mRNA by targeting them for decapping. LSM2 binds specifically to the 3'-terminal U-tract of U6 snRNA. LSM2-LSM8 probably is involved in processing of pre-tRNAs, pre-rRNAs and U3 snoRNA. LSM2, probably in a complex that contains LSM2-LSM7 but not LSM1 or LSM8, associates with the precursor of the RNA component of RNase P (pre-P RNA) and may be involved in maturing pre-P RNA. LSM2 is required for processing of pre-tRNAs, pre-rRNAs and U3 snoRNA.8 Publications

GO - Molecular functioni

  1. RNA binding Source: UniProtKB-KW
  2. protein binding Source: IntAct

GO - Biological processi

  1. mRNA splicing, via spliceosome Source: SGD
  2. rRNA processing Source: UniProtKB-KW
  3. tRNA processing Source: UniProtKB-KW
Complete GO annotation...

Keywords - Molecular functioni

Ribonucleoprotein

Keywords - Biological processi

mRNA processing, mRNA splicing, rRNA processing, tRNA processing

Keywords - Ligandi

RNA-binding

Enzyme and pathway databases

BioCyciYEAST:G3O-28929-MONOMER.
ReactomeiREACT_191540. mRNA Splicing - Minor Pathway.

Names & Taxonomyi

Protein namesi
Recommended name:
U6 snRNA-associated Sm-like protein LSm2
Alternative name(s):
Small nuclear ribonucleoprotein D homolog SNP3
Gene namesi
Name:LSM2
Synonyms:SMX5, SNP3
Ordered Locus Names:YBL026W
ORF Names:YBL0425
OrganismiSaccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast)
Taxonomic identifieri559292 [NCBI]
Taxonomic lineageiEukaryotaFungiDikaryaAscomycotaSaccharomycotinaSaccharomycetesSaccharomycetalesSaccharomycetaceaeSaccharomyces
ProteomesiUP000002311: Chromosome II

Organism-specific databases

CYGDiYBL026w.
SGDiS000000122. LSM2.

Subcellular locationi

Nucleus. Cytoplasm Inferred

GO - Cellular componenti

  1. U4/U6 x U5 tri-snRNP complex Source: SGD
  2. U6 snRNP Source: SGD
  3. cytoplasmic mRNA processing body Source: SGD
  4. nucleolus Source: SGD
  5. small nucleolar ribonucleoprotein complex Source: SGD
  6. spliceosomal complex Source: UniProtKB-KW
Complete GO annotation...

Keywords - Cellular componenti

Cytoplasm, Nucleus, Spliceosome

Pathology & Biotechi

Mutagenesis

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Mutagenesisi35 – 351F → A: Strongly reduces affinity for poly-U RNA ends. 1 Publication
Mutagenesisi37 – 371N → A: Strongly reduces affinity for poly-U RNA ends. 1 Publication
Mutagenesisi63 – 631R → A: Strongly reduces affinity for poly-U RNA ends. 2 Publications

PTM / Processingi

Molecule processing

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Chaini1 – 9595U6 snRNA-associated Sm-like protein LSm2
PRO_0000125559Add
BLAST

Proteomic databases

MaxQBiP38203.
PaxDbiP38203.
PeptideAtlasiP38203.

Expressioni

Gene expression databases

GenevestigatoriP38203.

Interactioni

Subunit structurei

Component of the heptameric LSM1-LSM7 complex that forms a seven-membered ring structure with a doughnut shape. The LSm subunits are arranged in the order LSM1, LSM2, LSM3, LSM6, LSM5, LSM7 and LSM4. Except for LSM1, where a C-terminal helix crosses the ring structure to form additional interactions with LSM3 and LSM6, each subunit interacts only with its two neighboring subunits. The LSM1-LSM7 complex interacts with PAT1; within the complex PAT1 has direct interactions with LSM2 and LSM3. Component of the heptameric LSM2-LSM8 complex that forms a seven-membered ring structure with a doughnut shape; an RNA strand can pass through the hole in the center of the ring structure. The LSm subunits are arranged in the order LSM8, LSM2, LSM3, LSM6, LSM5, LSM7 and LSM4. LSM2-LSM8 associates with PAT1 and XRN1. A complex comprising LSM2-LSM7 without LSM1 or LSM8 may exist. Likewise, LSM2 and LSM3 can assemble into a doughnut structure that binds PAT1 (in vitro). Component of the U4/U6-U5 tri-snRNP complex composed of the U4, U6 and U5 snRNAs and at least PRP3, PRP4, PRP6, PRP8, PRP18, PRP31, PRP38, SNU13, SNU23, SNU66, SNU114, SPP381, SMB1, SMD1, SMD2, SMD3, SMX2, SMX3, LSM2, LSM3, LSM4, LSM5, LSM6, LSM7, LSM8, BRR2 and DIB1.7 Publications

Binary interactionsi

WithEntry#Exp.IntActNotes
LSM1P470176EBI-180,EBI-174
LSM3P577434EBI-180,EBI-10227
LSM5P400894EBI-180,EBI-10236
LSM6Q064064EBI-180,EBI-196
LSM7P539053EBI-180,EBI-141
LSM8P470935EBI-180,EBI-313
PAT1P256444EBI-180,EBI-204

Protein-protein interaction databases

BioGridi32672. 92 interactions.
DIPiDIP-794N.
IntActiP38203. 65 interactions.
MINTiMINT-383549.
STRINGi4932.YBL026W.

Structurei

Secondary structure

Legend: HelixTurnBeta strand
Show more details
Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Helixi2 – 87
Turni9 – 124
Beta strandi13 – 197
Turni20 – 223
Beta strandi24 – 329
Beta strandi38 – 458
Beta strandi49 – 513
Beta strandi54 – 585
Beta strandi60 – 623
Helixi64 – 663
Beta strandi67 – 726
Helixi74 – 763
Helixi79 – 9315

3D structure databases

Select the link destinations:
PDBe
RCSB PDB
PDBj
Links Updated
EntryMethodResolution (Å)ChainPositionsPDBsum
4C8QX-ray3.70B2-95[»]
4C92X-ray2.30B2-95[»]
4M75X-ray2.95B/I1-95[»]
4M77X-ray3.11B/I1-95[»]
4M78X-ray2.79B/I1-95[»]
4M7AX-ray2.78B/I1-95[»]
4M7DX-ray2.60B/I1-95[»]
4N0AX-ray3.15C/D/G1-95[»]
ProteinModelPortaliP38203.
SMRiP38203. Positions 2-95.

Family & Domainsi

Sequence similaritiesi

Belongs to the snRNP Sm proteins family.

Phylogenomic databases

eggNOGiCOG1958.
GeneTreeiENSGT00390000016597.
HOGENOMiHOG000166937.
KOiK12621.
OMAiKLDNISC.
OrthoDBiEOG7PZSB0.

Family and domain databases

InterProiIPR010920. LSM_dom.
IPR001163. Ribonucl_LSM.
IPR006649. Ribonucl_LSM_euk/arc.
IPR016654. U6_snRNA_Lsm2.
[Graphical view]
PANTHERiPTHR13829. PTHR13829. 1 hit.
PfamiPF01423. LSM. 1 hit.
[Graphical view]
PIRSFiPIRSF016394. U6_snRNA_Lsm2. 1 hit.
SMARTiSM00651. Sm. 1 hit.
[Graphical view]
SUPFAMiSSF50182. SSF50182. 1 hit.

Sequencei

Sequence statusi: Complete.

P38203-1 [UniParc]FASTAAdd to Basket

« Hide

MLFFSFFKTL VDQEVVVELK NDIEIKGTLQ SVDQFLNLKL DNISCTDEKK   50
YPHLGSVRNI FIRGSTVRYV YLNKNMVDTN LLQDATRREV MTERK 95
Length:95
Mass (Da):11,163
Last modified:October 1, 1994 - v1
Checksum:iC23856268CEE92E2
GO

Sequence databases

Select the link destinations:
EMBL
GenBank
DDBJ
Links Updated
X77291 Genomic DNA. Translation: CAA54505.1.
Z35787 Genomic DNA. Translation: CAA84845.1.
BK006936 Genomic DNA. Translation: DAA07094.1.
PIRiS45760.
RefSeqiNP_009527.1. NM_001178266.1.

Genome annotation databases

EnsemblFungiiYBL026W; YBL026W; YBL026W.
GeneIDi852255.
KEGGisce:YBL026W.

Cross-referencesi

Sequence databases

Select the link destinations:
EMBL
GenBank
DDBJ
Links Updated
X77291 Genomic DNA. Translation: CAA54505.1 .
Z35787 Genomic DNA. Translation: CAA84845.1 .
BK006936 Genomic DNA. Translation: DAA07094.1 .
PIRi S45760.
RefSeqi NP_009527.1. NM_001178266.1.

3D structure databases

Select the link destinations:
PDBe
RCSB PDB
PDBj
Links Updated
Entry Method Resolution (Å) Chain Positions PDBsum
4C8Q X-ray 3.70 B 2-95 [» ]
4C92 X-ray 2.30 B 2-95 [» ]
4M75 X-ray 2.95 B/I 1-95 [» ]
4M77 X-ray 3.11 B/I 1-95 [» ]
4M78 X-ray 2.79 B/I 1-95 [» ]
4M7A X-ray 2.78 B/I 1-95 [» ]
4M7D X-ray 2.60 B/I 1-95 [» ]
4N0A X-ray 3.15 C/D/G 1-95 [» ]
ProteinModelPortali P38203.
SMRi P38203. Positions 2-95.
ModBasei Search...
MobiDBi Search...

Protein-protein interaction databases

BioGridi 32672. 92 interactions.
DIPi DIP-794N.
IntActi P38203. 65 interactions.
MINTi MINT-383549.
STRINGi 4932.YBL026W.

Proteomic databases

MaxQBi P38203.
PaxDbi P38203.
PeptideAtlasi P38203.

Protocols and materials databases

Structural Biology Knowledgebase Search...

Genome annotation databases

EnsemblFungii YBL026W ; YBL026W ; YBL026W .
GeneIDi 852255.
KEGGi sce:YBL026W.

Organism-specific databases

CYGDi YBL026w.
SGDi S000000122. LSM2.

Phylogenomic databases

eggNOGi COG1958.
GeneTreei ENSGT00390000016597.
HOGENOMi HOG000166937.
KOi K12621.
OMAi KLDNISC.
OrthoDBi EOG7PZSB0.

Enzyme and pathway databases

BioCyci YEAST:G3O-28929-MONOMER.
Reactomei REACT_191540. mRNA Splicing - Minor Pathway.

Miscellaneous databases

NextBioi 970835.
PROi P38203.

Gene expression databases

Genevestigatori P38203.

Family and domain databases

InterProi IPR010920. LSM_dom.
IPR001163. Ribonucl_LSM.
IPR006649. Ribonucl_LSM_euk/arc.
IPR016654. U6_snRNA_Lsm2.
[Graphical view ]
PANTHERi PTHR13829. PTHR13829. 1 hit.
Pfami PF01423. LSM. 1 hit.
[Graphical view ]
PIRSFi PIRSF016394. U6_snRNA_Lsm2. 1 hit.
SMARTi SM00651. Sm. 1 hit.
[Graphical view ]
SUPFAMi SSF50182. SSF50182. 1 hit.
ProtoNeti Search...

Publicationsi

« Hide 'large scale' publications
  1. "Analysis of a 17.4 kb DNA segment of yeast chromosome II encompassing the ribosomal protein L19 as well as proteins with homologies to components of the hnRNP and snRNP complexes and to the human proliferation-associated p120 antigen."
    van Dyck L., Jonniaux J.-L., Barreiros T.D.M., Kleine K., Goffeau A.
    Yeast 10:1663-1673(1994) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA].
    Strain: ATCC 204508 / S288c.
  2. "Complete DNA sequence of yeast chromosome II."
    Feldmann H., Aigle M., Aljinovic G., Andre B., Baclet M.C., Barthe C., Baur A., Becam A.-M., Biteau N., Boles E., Brandt T., Brendel M., Brueckner M., Bussereau F., Christiansen C., Contreras R., Crouzet M., Cziepluch C.
    , Demolis N., Delaveau T., Doignon F., Domdey H., Duesterhus S., Dubois E., Dujon B., El Bakkoury M., Entian K.-D., Feuermann M., Fiers W., Fobo G.M., Fritz C., Gassenhuber J., Glansdorff N., Goffeau A., Grivell L.A., de Haan M., Hein C., Herbert C.J., Hollenberg C.P., Holmstroem K., Jacq C., Jacquet M., Jauniaux J.-C., Jonniaux J.-L., Kallesoee T., Kiesau P., Kirchrath L., Koetter P., Korol S., Liebl S., Logghe M., Lohan A.J.E., Louis E.J., Li Z.Y., Maat M.J., Mallet L., Mannhaupt G., Messenguy F., Miosga T., Molemans F., Mueller S., Nasr F., Obermaier B., Perea J., Pierard A., Piravandi E., Pohl F.M., Pohl T.M., Potier S., Proft M., Purnelle B., Ramezani Rad M., Rieger M., Rose M., Schaaff-Gerstenschlaeger I., Scherens B., Schwarzlose C., Skala J., Slonimski P.P., Smits P.H.M., Souciet J.-L., Steensma H.Y., Stucka R., Urrestarazu L.A., van der Aart Q.J.M., Van Dyck L., Vassarotti A., Vetter I., Vierendeels F., Vissers S., Wagner G., de Wergifosse P., Wolfe K.H., Zagulski M., Zimmermann F.K., Mewes H.-W., Kleine K.
    EMBO J. 13:5795-5809(1994) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
    Strain: ATCC 204508 / S288c.
  3. Cited for: GENOME REANNOTATION.
    Strain: ATCC 204508 / S288c.
  4. "Sm and Sm-like proteins assemble in two related complexes of deep evolutionary origin."
    Salgado-Garrido J., Bragado-Nilsson E., Kandels-Lewis S., Seraphin B.
    EMBO J. 18:3451-3462(1999) [PubMed] [Europe PMC] [Abstract]
    Cited for: IDENTIFICATION IN THE LSM2-LSM8 COMPLEX, ASSOCIATION WITH PRE-P RNA.
  5. "Characterization of Sm-like proteins in yeast and their association with U6 snRNA."
    Mayes A.E., Verdone L., Legrain P., Beggs J.D.
    EMBO J. 18:4321-4331(1999) [PubMed] [Europe PMC] [Abstract]
    Cited for: CHARACTERIZATION.
  6. "Identification by mass spectrometry and functional analysis of novel proteins of the yeast [U4/U6.U5] tri-snRNP."
    Gottschalk A., Neubauer G., Banroques J., Mann M., Luehrmann R., Fabrizio P.
    EMBO J. 18:4535-4548(1999) [PubMed] [Europe PMC] [Abstract]
    Cited for: SUBUNIT, IDENTIFICATION IN THE U4/U5/U6 TRI-SNRNP COMPLEX, IDENTIFICATION BY MASS SPECTROMETRY.
  7. "A Sm-like protein complex that participates in mRNA degradation."
    Bouveret E., Rigaut G., Shevchenko A., Wilm M., Seraphin B.
    EMBO J. 19:1661-1671(2000) [PubMed] [Europe PMC] [Abstract]
    Cited for: IDENTIFICATION IN THE LSM1-LSM7 COMPLEX, ASSOCIATION OF THE LSM1-LSM7 COMPLEX WITH PAT1 AND XRN1, FUNCTION OF THE LSM1-LSM7 COMPLEX, IDENTIFICATION IN THE LSM2-LSM8 COMPLEX, ASSOCIATION OF THE LSM2-LSM8 COMPLEX WITH U6 SNRNA, IDENTIFICATION BY MASS SPECTROMETRY.
  8. "Lsm proteins are required for normal processing of pre-tRNAs and their efficient association with La-homologous protein Lhp1p."
    Kufel J., Allmang C., Verdone L., Beggs J.D., Tollervey D.
    Mol. Cell. Biol. 22:5248-5256(2002) [PubMed] [Europe PMC] [Abstract]
    Cited for: FUNCTION IN PROCESSING OF PRE-TRNAS.
  9. "Lsm Proteins are required for normal processing and stability of ribosomal RNAs."
    Kufel J., Allmang C., Petfalski E., Beggs J.D., Tollervey D.
    J. Biol. Chem. 278:2147-2156(2003) [PubMed] [Europe PMC] [Abstract]
    Cited for: FUNCTION IN PROCESSING OF PRE-RRNAS.
  10. Cited for: LEVEL OF PROTEIN EXPRESSION [LARGE SCALE ANALYSIS].
  11. "A complex pathway for 3' processing of the yeast U3 snoRNA."
    Kufel J., Allmang C., Verdone L., Beggs J., Tollervey D.
    Nucleic Acids Res. 31:6788-6797(2003) [PubMed] [Europe PMC] [Abstract]
    Cited for: FUNCTION IN PROCESSING OF U3 SNORNA.
  12. "Nuclear pre-mRNA decapping and 5' degradation in yeast require the Lsm2-8p complex."
    Kufel J., Bousquet-Antonelli C., Beggs J.D., Tollervey D.
    Mol. Cell. Biol. 24:9646-9657(2004) [PubMed] [Europe PMC] [Abstract]
    Cited for: FUNCTION OF THE LSM2-LSM8 COMPLEX IN NUCLEAR MRNA DEGRADATION.
  13. "Architecture of the Lsm1-7-Pat1 complex: a conserved assembly in eukaryotic mRNA turnover."
    Sharif H., Conti E.
    Cell Rep. 5:283-291(2013) [PubMed] [Europe PMC] [Abstract]
    Cited for: X-RAY CRYSTALLOGRAPHY (2.30 ANGSTROMS) OF 27-172 OF LSM1-LSM7 COMPLEX, SUBUNIT, INTERACTION WITH PAT1.
  14. "Crystal structure and biochemical analysis of the heptameric Lsm1-7 complex."
    Zhou L., Zhou Y., Hang J., Wan R., Lu G., Yan C., Shi Y.
    Cell Res. 24:497-500(2014) [PubMed] [Europe PMC] [Abstract]
    Cited for: X-RAY CRYSTALLOGRAPHY (2.95 ANGSTROMS) OF LSM1-LSM7 COMPLEX, SUBUNIT, FUNCTION, RNA-BINDING, MUTAGENESIS OF ARG-63.
  15. "Lsm2 and Lsm3 bridge the interaction of the Lsm1-7 complex with Pat1 for decapping activation."
    Wu D., Muhlrad D., Bowler M.W., Jiang S., Liu Z., Parker R., Song H.
    Cell Res. 24:233-246(2014) [PubMed] [Europe PMC] [Abstract]
    Cited for: X-RAY CRYSTALLOGRAPHY (3.15 ANGSTROMS), SUBUNIT, INTERACTION WITH PAT1, FUNCTION, RNA-BINDING.
  16. "Crystal structures of the Lsm complex bound to the 3' end sequence of U6 small nuclear RNA."
    Zhou L., Hang J., Zhou Y., Wan R., Lu G., Yin P., Yan C., Shi Y.
    Nature 506:116-120(2014) [PubMed] [Europe PMC] [Abstract]
    Cited for: X-RAY CRYSTALLOGRAPHY (2.60 ANGSTROMS) OF LSM2-LSM8 COMPLEX, SUBUNIT, FUNCTION, RNA-BINDING, MUTAGENESIS OF PHE-35; ASN-37 AND ARG-63.

Entry informationi

Entry nameiLSM2_YEAST
AccessioniPrimary (citable) accession number: P38203
Secondary accession number(s): D6VPX4
Entry historyi
Integrated into UniProtKB/Swiss-Prot: October 1, 1994
Last sequence update: October 1, 1994
Last modified: September 3, 2014
This is version 125 of the entry and version 1 of the sequence. [Complete history]
Entry statusiReviewed (UniProtKB/Swiss-Prot)
Annotation programFungal Protein Annotation Program

Miscellaneousi

Miscellaneous

Present with 2210 molecules/cell in log phase SD medium.

Keywords - Technical termi

3D-structure, Complete proteome, Reference proteome

Documents

  1. PDB cross-references
    Index of Protein Data Bank (PDB) cross-references
  2. SIMILARITY comments
    Index of protein domains and families
  3. Yeast
    Yeast (Saccharomyces cerevisiae): entries, gene names and cross-references to SGD
  4. Yeast chromosome II
    Yeast (Saccharomyces cerevisiae) chromosome II: entries and gene names

External Data

Dasty 3

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